Abstract

Aromatic compounds belong to one of the most widely distributed classes of organic compounds in nature, and a significant number of xenobiotics belong to this family of compounds. Since many habitats containing large amounts of aromatic compounds are often anoxic, the anaerobic catabolism of aromatic compounds by microorganisms becomes crucial in biogeochemical cycles and in the sustainable development of the biosphere. The mineralization of aromatic compounds by facultative or obligate anaerobic bacteria can be coupled to anaerobic respiration with a variety of electron acceptors as well as to fermentation and anoxygenic photosynthesis. Since the redox potential of the electron-accepting system dictates the degradative strategy, there is wide biochemical diversity among anaerobic aromatic degraders. However, the genetic determinants of all these processes and the mechanisms involved in their regulation are much less studied. This review focuses on the recent findings that standard molecular biology approaches together with new high-throughput technologies (e.g., genome sequencing, transcriptomics, proteomics, and metagenomics) have provided regarding the genetics, regulation, ecophysiology, and evolution of anaerobic aromatic degradation pathways. These studies revealed that the anaerobic catabolism of aromatic compounds is more diverse and widespread than previously thought, and the complex metabolic and stress programs associated with the use of aromatic compounds under anaerobic conditions are starting to be unraveled. Anaerobic biotransformation processes based on unprecedented enzymes and pathways with novel metabolic capabilities, as well as the design of novel regulatory circuits and catabolic networks of great biotechnological potential in synthetic biology, are now feasible to approach.

The anaerobic catabolic funnel for monoaromatic compounds. A broad range of aromatic compounds funnel through a wide variety of peripheral pathways (black arrows) into a limited number of aromatic central intermediates, e.g., benzoyl-CoA (BzCoA), 2-aminobenzoyl-CoA (2-AminoBzCoA), 3-hydroxybenzoyl-CoA (3-HydroxyBzCoA), 3-methylbenzoyl-CoA (3-MethylBzCoA), 6-hydroxynicotinate, resorcinol, phloroglucinol, and HHQ, which are then dearomatized and channeled by the cognate central pathways (thin arrows) to the central metabolism of the cell. The dearomatization of the central intermediates can involve a ferredoxin (Fd) and energy (e.g., ATP) (red arrows), a ferredoxin (blue arrows), or NAD(P)H (green arrows) as electron donors. An oxidative dearomatization of HHQ has also been described (yellow arrow). It should be noted that the same aromatic compound can be degraded following different peripheral and central pathways depending on the particular redox potential of the final electron-accepting system in the host cell.

Proposed pathway for anaerobic catabolism of l-phenylalanine to phenylacetate in Thauera and Azoarcus strains. (A) Enzymatic reactions of the pathway according to data described previously by Schneider et al. () and Wöhlbrand et al. (). The enzymes involved are l-phenylalanine:2-oxoglutarate transaminase (Pat), phenylpyruvate decarboxylase (Pdc), and phenylacetaldehyde oxidoreductase (AOR). Fdx (ferredoxin) and Fdx:NADH oxidoreductase are predicted to be auxiliary enzymes of AOR (). (B) Organization of the genes likely to be involved in anaerobic catabolism of phenylalanine to phenylacetate in Azoarcus sp. strain EbN1 (GenBank accession number NC_006513). Genes are represented by arrows: red, pat gene, encoding the putative l-phenylalanine:2-oxoglutarate transaminase; blue, pdc gene, encoding the putative phenylpyruvate decarboxylase; green, genes encoding a putative phenylacetaldehyde oxidoreductase AOR and the ferredoxin and ferredoxin:NADH oxidoreductase enzymes. Two vertical lines mean that the genes are not adjacent in the genome.

Comparative distribution of the gene clusters involved in anaerobic catabolism of aromatic compounds in different bacterial chromosomes. Characterized or predicted gene clusters for the anaerobic degradation of different aromatic (and cyclohexane carboxylate) compounds are indicated with a different color code. The supraoperonic clustering (26 kb) and the catabolic island (300 kb) of R. palustris (RPA0650 to RPA0673) and G. metallireducens (gmet2037 to gmet2284), respectively, are boxed and expanded. The gene arrangements within the clusters are shown in detail in Fig. to .

Transcriptional organization and regulation of the ali-bad-hba supraoperonic cluster of R. palustris. The ali, bad, and hba genes are represented by yellow, blue, and green boxes, respectively. The enzymes encoded by the ali, bad, and hba genes and the reactions catalyzed by these enzymes are boxed with yellow, blue, and green, respectively. The badR, badM, and hbaR regulatory genes and the corresponding BadR, BadM, and HbaR regulators, respectively, are indicated in red. The AadR regulatory protein, which is encoded outside the clustering, is also shown (violet). The arrows at the top of the genes indicate that these genes constitute an operon (solid arrows) or a putative operon (dashed arrows). The badD, hbaA, and hbaR promoters that were reported to be controlled by the transcriptional regulators are shown (red bent arrows). The − and + symbols indicate transcriptional repression and activation, respectively.

Transcriptional organization and regulation of the bzd cluster of Azoarcus sp. strain CIB. The genes are grouped into two operons, the bzdR regulatory operon (blue) and the bzdNOPQMSTUVWXYZA catabolic operon (orange), controlled by the PR and PN promoters, respectively. Both promoters are repressed by the BzdR protein (blue), with benzoyl-CoA being the inducer molecule. The activation of the PN promoter under anaerobic conditions is also dependent on the AcpR protein (violet). Some carbon sources, such as organic acids, cause catabolite repression at the PN promoter via BzdR and a still-unknown factor (?). The − and + symbols represent transcriptional repression and activation, respectively.